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          differential regulation for RNA-Seq</title>
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           <a href="./index.html"><h1>Illumina iGenomes</h1></a>
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        <a href="http://www.mcb.berkeley.edu/">
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            border=0 src="images/UCBerkeley-seal.scaled.gif">
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        <a href="http://genomics.jhu.edu/">
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          <h2>Site Map</h2>
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              <li><a href="index.html">Home</a></li>
              <li><a href="tutorial.html">Getting started</a></li>
              <li><a href="manual.html">Manual</a></li>
              <li><a href="howitworks.html">How Cufflinks works</a></li>
			  <li><a href="igenomes.html">Index and annotation downloads</a></li>
              <li><a href="faq.html">FAQ</a></li>
			  <li><a href="http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html">Protocol</a></li>
			  <li><a href="report.html">Benchmarking</a></li>
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          <h2><u>News and updates</u></h2>
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                    <td>New releases and related tools will be announced
                      through the <a
                        href="https://lists.sourceforge.net/lists/listinfo/bowtie-bio-announce"><b>mailing
                          list</b></a></td>
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          <h2><u>Getting Help</u></h2>
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                    <td>Questions about Cufflinks and Cuffdiff should be posted on our <a href="https://groups.google.com/forum/#!forum/tuxedo-tools-users"><b>Google Group</b></a>. Please use <a
                        href="mailto:tophat.cufflinks@gmail.com">tophat.cufflinks@gmail.com</a> for private communications only.
                      Please do not email technical questions to
                      Cufflinks contributors directly.</td>
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          <a href="./downloads">
            <h2><u>Releases</u></h2>
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                    <td>version 2.2.0</td>
                    <td align="right">5/25/2014</td>
                  </tr>
                  <tr>
                    <td><a href="./downloads/cufflinks-2.2.0.tar.gz"
                        onclick="javascript:
                        pageTracker._trackPageview('/downloads/cufflinks_source');
                        ">&nbsp;&nbsp;&nbsp;Source code</a></td>
                  </tr>
                  <tr>
                    <td><a
                        href="./downloads/cufflinks-2.2.0.Linux_x86_64.tar.gz"
                        onclick="javascript:
                        pageTracker._trackPageview('/downloads/cufflinks');
                        ">&nbsp;&nbsp;&nbsp;Linux x86_64 binary</a></td>
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                    <td><a
                        href="./downloads/cufflinks-2.2.0.OSX_x86_64.tar.gz"
                        onclick="javascript:
                        pageTracker._trackPageview('/downloads/cufflinks');
                        ">&nbsp;&nbsp;&nbsp;Mac OS X x86_64 binary</a></td>
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                </tbody>
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            </ul>
          </div>         

		  <h2>Related Tools</h2>
          <div class="box">
            <ul>
                <li><a href="http://monocle-bio.sourceforge.net">Monocle</a>:
                  Single-cell RNA-Seq analysis</li>
				<li><a href="http://compbio.mit.edu/cummeRbund/">CummeRbund</a>:
	                Visualization of RNA-Seq differential analysis</li>
              <li><a href="http://tophat.cbcb.umd.edu/">TopHat</a>:
                Alignment of short RNA-Seq reads</li>
              <li><a href="http://bowtie.cbcb.umd.edu">Bowtie</a>:
                Ultrafast short read alignment</li>
            </ul>
          </div>



         <h2>Publications</h2>
          <div class="box">
            <ul>
              <li style="font-size: x-small; line-height: 130%">
                <p>Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan
                  G, van Baren MJ, Salzberg SL, Wold B, Pachter L.<b> <a
                      href="http://dx.doi.org/10.1038/nbt.1621">Transcript
                      assembly and quantification by RNA-Seq reveals
                      unannotated transcripts and isoform switching
                      during cell differentiation</a></b> <br>
                  <i><a href="http://www.nature.com/nbt">Nature
                      Biotechnology</a></i> doi:10.1038/nbt.1621</p>
                <br>
              </li>
              <li style="font-size: x-small; line-height: 130%">
                <p>Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter
                  L.<b> <a
                      href="http://genomebiology.com/2011/12/3/R22/abstract">Improving
                      RNA-Seq expression estimates by correcting for
                      fragment bias</a></b> <br>
                  <i><a href="http://www.genomebiology.com">Genome
                      Biology</a></i> doi:10.1186/gb-2011-12-3-r22</p>
                <br>
              </li>
              <li style="font-size: x-small; line-height: 130%">
                <p>Roberts A, Pimentel H, Trapnell C, Pachter
                  L.<b> <a
                      href="http://bioinformatics.oxfordjournals.org/content/early/2011/06/21/bioinformatics.btr355.abstract">
                      Identification of novel transcripts in annotated genomes using RNA-Seq</a></b> <br>
                  <i><a href="http://bioinformatics.oxfordjournals.org/">Bioinformatics</a></i> doi:10.1093/bioinformatics/btr355</p>
                <br>
              </li>
			  <li style="font-size: x-small; line-height: 130%">
                <p>Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L<b> <a
                      href="http://dx.doi.org/10.1038/nbt.2450">Differential 
					 analysis of gene regulation at transcript resolution with RNA-seq
					</a></b> <br>
                  <i><a href="http://www.nature.com/nbt">Nature
                      Biotechnology</a></i> doi:10.1038/nbt.2450</p>
                <br>
              </li>
            </ul>
          </div>
          <h2>Contributors</h2>
          <div class="box">
            <ul>
              <li><a href="http://www.cs.umd.edu/%7Ecole/">Cole Trapnell</a></li>
              <li><a href="http://www.cs.berkeley.edu/%7Eadarob/">Adam
                  Roberts</a></li>
              <li>Geo Pertea</li>
			  <li>David Hendrickson<li>
			  <li>Loyal Goff</li>
			  <li>Martin Sauvageau</li>
              <li>Brian Williams</li>
              <li><a href="http://wormlab.caltech.edu/members/">Ali
                  Mortazavi</a></li>
              <li>Gordon Kwan</li>
              <li>Jeltje van Baren</li>
			  <li><a href="http://www.rinnlab.com">John Rinn</a></li>
              <li><a href="http://www.cbcb.umd.edu/%7Esalzberg/">Steven
                  Salzberg</a></li>
              <li><a href="http://biology.caltech.edu/Members/Wold">Barbara
                  Wold</a></li>
              <li><a href="http://www.math.berkeley.edu/%7Elpachter/">Lior
                  Pachter</a></li>
            </ul>
          </div>
         <h2>Links</h2>
         <div class="box">
           <ul>
             <li><a href="http://bio.math.berkeley.edu/">Berkeley LMCB</a></li>
             <li><a href="http://www.cbcb.umd.edu/">UMD CBCB</a></li>
             <li><a href="http://woldlab.caltech.edu/">Wold Lab</a></li>
           </ul>
         </div>
       </div>
      
    </div> <!-- End of "rightside" -->
    <div id="leftside">
    Illumina has provided the RNA-Seq user community with a set of genome sequence indexes (including Bowtie indexes) as well as GTF transcript annotation files.  These files can be used with TopHat and Cufflinks to quickly perform expression analysis and gene discovery.  The annotation files are augmented with the <tt>tss_id</tt> and <tt>p_id</tt> GTF attributes that Cufflinks needs to perform differential splicing, CDS output, and promoter user analysis. We recommend that you download your Bowtie indexes and annotation files from this page. More information about Illumina's iGenomes project can be found <A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/README.txt">here</A>.
    <br/>
    <br/>
    <TABLE id="box-table-a" CELLPADDING=3>
      
      <TR>
<TH ALIGN="LEFT">Organism</TH>
<TH ALIGN="LEFT">Data source</TH>
<TH ALIGN="LEFT">Version</TH>
<TH ALIGN="LEFT">Size</TH>
<TH ALIGN="LEFT">Last Modified</TH>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=6>Homo sapiens</TD>
<TD ALIGN="LEFT" rowspan=1>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/Ensembl/GRCh37/Homo_sapiens_Ensembl_GRCh37.tar.gz">GRCh37</A></TD>
<TD ALIGN="RIGHT">17297 MB</TD>
<TD ALIGN="LEFT">May 14 17:23</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=3>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/build36.3/Homo_sapiens_NCBI_build36.3.tar.gz">build36.3</A></TD>
<TD ALIGN="RIGHT">15814 MB</TD>
<TD ALIGN="LEFT">May 14 19:36</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/build37.1/Homo_sapiens_NCBI_build37.1.tar.gz">build37.1</A></TD>
<TD ALIGN="RIGHT">15850 MB</TD>
<TD ALIGN="LEFT">May 14 19:04</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/build37.2/Homo_sapiens_NCBI_build37.2.tar.gz">build37.2</A></TD>
<TD ALIGN="RIGHT">21450 MB</TD>
<TD ALIGN="LEFT">May 14 17:54</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg18/Homo_sapiens_UCSC_hg18.tar.gz">hg18</A></TD>
<TD ALIGN="RIGHT">17349 MB</TD>
<TD ALIGN="LEFT">May 14 15:31</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz">hg19</A></TD>
<TD ALIGN="RIGHT">21058 MB</TD>
<TD ALIGN="LEFT">May 14 15:36</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=5>Mus musculus</TD>
<TD ALIGN="LEFT" rowspan=1>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/Ensembl/NCBIM37/Mus_musculus_Ensembl_NCBIM37.tar.gz">NCBIM37</A></TD>
<TD ALIGN="RIGHT">14428 MB</TD>
<TD ALIGN="LEFT">May 14 22:13</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/NCBI/build37.1/Mus_musculus_NCBI_build37.1.tar.gz">build37.1</A></TD>
<TD ALIGN="RIGHT">15260 MB</TD>
<TD ALIGN="LEFT">May 15 17:53</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/NCBI/build37.2/Mus_musculus_NCBI_build37.2.tar.gz">build37.2</A></TD>
<TD ALIGN="RIGHT">15725 MB</TD>
<TD ALIGN="LEFT">May 14 22:52</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm9/Mus_musculus_UCSC_mm9.tar.gz">mm9</A></TD>
<TD ALIGN="RIGHT">14537 MB</TD>
<TD ALIGN="LEFT">May 14 21:12</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/UCSC/mm10/Mus_musculus_UCSC_mm10.tar.gz">mm10</A></TD>
<TD ALIGN="RIGHT">14193 MB</TD>
<TD ALIGN="LEFT">Jun 14 11:29</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=3>Rattus norvegicus</TD>
<TD ALIGN="LEFT" rowspan=1>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Rattus_norvegicus/Ensembl/RGSC3.4/Rattus_norvegicus_Ensembl_RGSC3.4.tar.gz">RGSC3.4</A></TD>
<TD ALIGN="RIGHT">13725 MB</TD>
<TD ALIGN="LEFT">May 15 22:33</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=1>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Rattus_norvegicus/NCBI/RGSC_v3.4/Rattus_norvegicus_NCBI_RGSC_v3.4.tar.gz">RGSC_v3.4</A></TD>
<TD ALIGN="RIGHT">14234 MB</TD>
<TD ALIGN="LEFT">May 15 23:58</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=1>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Rattus_norvegicus/UCSC/rn4/Rattus_norvegicus_UCSC_rn4.tar.gz">rn4</A></TD>
<TD ALIGN="RIGHT">13710 MB</TD>
<TD ALIGN="LEFT">May 15 22:32</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=6>Bos taurus</TD>
<TD ALIGN="LEFT" rowspan=2>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Bos_taurus/Ensembl/Btau_4.0/Bos_taurus_Ensembl_Btau_4.0.tar.gz">Btau_4.0</A></TD>
<TD ALIGN="RIGHT">13315 MB</TD>
<TD ALIGN="LEFT">May 11 14:18</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Bos_taurus/Ensembl/UMD3.1/Bos_taurus_Ensembl_UMD3.1.tar.gz">UMD3.1</A></TD>
<TD ALIGN="RIGHT">14042 MB</TD>
<TD ALIGN="LEFT">May 11 12:41</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=3>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Bos_taurus/NCBI/Btau_4.2/Bos_taurus_NCBI_Btau_4.2.tar.gz">Btau_4.2</A></TD>
<TD ALIGN="RIGHT">13357 MB</TD>
<TD ALIGN="LEFT">May 11 14:11</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Bos_taurus/NCBI/Btau_4.6.1/Bos_taurus_NCBI_Btau_4.6.1.tar.gz">Btau_4.6.1</A></TD>
<TD ALIGN="RIGHT">13448 MB</TD>
<TD ALIGN="LEFT">May 11 16:09</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Bos_taurus/NCBI/UMD_3.1/Bos_taurus_NCBI_UMD_3.1.tar.gz">UMD_3.1</A></TD>
<TD ALIGN="RIGHT">13990 MB</TD>
<TD ALIGN="LEFT">May 11 16:08</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=1>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Bos_taurus/UCSC/bosTau4/Bos_taurus_UCSC_bosTau4.tar.gz">bosTau4</A></TD>
<TD ALIGN="RIGHT">13386 MB</TD>
<TD ALIGN="LEFT">May 11 12:36</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=4>Canis familiaris</TD>
<TD ALIGN="LEFT" rowspan=1>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Canis_familiaris/Ensembl/BROADD2/Canis_familiaris_Ensembl_BROADD2.tar.gz">BROADD2</A></TD>
<TD ALIGN="RIGHT">13087 MB</TD>
<TD ALIGN="LEFT">May 11 18:00</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Canis_familiaris/NCBI/build2.1/Canis_familiaris_NCBI_build2.1.tar.gz">build2.1</A></TD>
<TD ALIGN="RIGHT">12847 MB</TD>
<TD ALIGN="LEFT">May 11 19:22</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Canis_familiaris/NCBI/build3.1/Canis_familiaris_NCBI_build3.1.tar.gz">build3.1</A></TD>
<TD ALIGN="RIGHT">12528 MB</TD>
<TD ALIGN="LEFT">May 11 19:30</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=1>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Canis_familiaris/UCSC/canFam2/Canis_familiaris_UCSC_canFam2.tar.gz">canFam2</A></TD>
<TD ALIGN="RIGHT">13138 MB</TD>
<TD ALIGN="LEFT">May 11 17:50</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=4>Gallus gallus</TD>
<TD ALIGN="LEFT" rowspan=1>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Gallus_gallus/Ensembl/WASHUC2/Gallus_gallus_Ensembl_WASHUC2.tar.gz">WASHUC2</A></TD>
<TD ALIGN="RIGHT">5547 MB</TD>
<TD ALIGN="LEFT">May 14 12:30</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Gallus_gallus/NCBI/build2.1/Gallus_gallus_NCBI_build2.1.tar.gz">build2.1</A></TD>
<TD ALIGN="RIGHT">5592 MB</TD>
<TD ALIGN="LEFT">May 14 13:08</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Gallus_gallus/NCBI/build3.1/Gallus_gallus_NCBI_build3.1.tar.gz">build3.1</A></TD>
<TD ALIGN="RIGHT">5469 MB</TD>
<TD ALIGN="LEFT">May 14 13:18</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=1>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Gallus_gallus/UCSC/galGal3/Gallus_gallus_UCSC_galGal3.tar.gz">galGal3</A></TD>
<TD ALIGN="RIGHT">5546 MB</TD>
<TD ALIGN="LEFT">May 14 11:52</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=6>Drosophila melanogaster</TD>
<TD ALIGN="LEFT" rowspan=2>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Drosophila_melanogaster/Ensembl/BDGP5/Drosophila_melanogaster_Ensembl_BDGP5.tar.gz">BDGP5</A></TD>
<TD ALIGN="RIGHT">669 MB</TD>
<TD ALIGN="LEFT">May 11 19:35</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Drosophila_melanogaster/Ensembl/BDGP5.25/Drosophila_melanogaster_Ensembl_BDGP5.25.tar.gz">BDGP5.25</A></TD>
<TD ALIGN="RIGHT">692 MB</TD>
<TD ALIGN="LEFT">May 11 19:32</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=3>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Drosophila_melanogaster/NCBI/build4.1/Drosophila_melanogaster_NCBI_build4.1.tar.gz">build4.1</A></TD>
<TD ALIGN="RIGHT">701 MB</TD>
<TD ALIGN="LEFT">May 11 19:38</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Drosophila_melanogaster/NCBI/build5/Drosophila_melanogaster_NCBI_build5.tar.gz">build5</A></TD>
<TD ALIGN="RIGHT">701 MB</TD>
<TD ALIGN="LEFT">May 11 19:41</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Drosophila_melanogaster/NCBI/build5.3/Drosophila_melanogaster_NCBI_build5.3.tar.gz">build5.3</A></TD>
<TD ALIGN="RIGHT">674 MB</TD>
<TD ALIGN="LEFT">May 11 19:40</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=1>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Drosophila_melanogaster/UCSC/dm3/Drosophila_melanogaster_UCSC_dm3.tar.gz">dm3</A></TD>
<TD ALIGN="RIGHT">763 MB</TD>
<TD ALIGN="LEFT">May 11 19:28</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=4>Arabidopsis thaliana</TD>
<TD ALIGN="LEFT" rowspan=2>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Arabidopsis_thaliana/Ensembl/TAIR9/Arabidopsis_thaliana_Ensembl_TAIR9.tar.gz">TAIR9</A></TD>
<TD ALIGN="RIGHT">710 MB</TD>
<TD ALIGN="LEFT">May 11 10:47</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Arabidopsis_thaliana/Ensembl/TAIR10/Arabidopsis_thaliana_Ensembl_TAIR10.tar.gz">TAIR10</A></TD>
<TD ALIGN="RIGHT">679 MB</TD>
<TD ALIGN="LEFT">May 11 10:46</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Arabidopsis_thaliana/NCBI/build9.1/Arabidopsis_thaliana_NCBI_build9.1.tar.gz">build9.1</A></TD>
<TD ALIGN="RIGHT">721 MB</TD>
<TD ALIGN="LEFT">May 11 10:51</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Arabidopsis_thaliana/NCBI/TAIR10/Arabidopsis_thaliana_NCBI_TAIR10.tar.gz">TAIR10</A></TD>
<TD ALIGN="RIGHT">658 MB</TD>
<TD ALIGN="LEFT">May 11 10:51</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=6>Caenorhabditis elegans</TD>
<TD ALIGN="LEFT" rowspan=2>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WS210/Caenorhabditis_elegans_Ensembl_WS210.tar.gz">WS210</A></TD>
<TD ALIGN="RIGHT">597 MB</TD>
<TD ALIGN="LEFT">May 11 16:16</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WS220/Caenorhabditis_elegans_Ensembl_WS220.tar.gz">WS220</A></TD>
<TD ALIGN="RIGHT">560 MB</TD>
<TD ALIGN="LEFT">May 11 16:17</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/NCBI/WS190/Caenorhabditis_elegans_NCBI_WS190.tar.gz">WS190</A></TD>
<TD ALIGN="RIGHT">566 MB</TD>
<TD ALIGN="LEFT">May 11 16:21</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/NCBI/WS195/Caenorhabditis_elegans_NCBI_WS195.tar.gz">WS195</A></TD>
<TD ALIGN="RIGHT">554 MB</TD>
<TD ALIGN="LEFT">May 11 16:21</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/UCSC/ce6/Caenorhabditis_elegans_UCSC_ce6.tar.gz">ce6</A></TD>
<TD ALIGN="RIGHT">617 MB</TD>
<TD ALIGN="LEFT">May 11 16:13</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/UCSC/ce10/Caenorhabditis_elegans_UCSC_ce10.tar.gz">ce10</A></TD>
<TD ALIGN="RIGHT">552 MB</TD>
<TD ALIGN="LEFT">May 11 16:12</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=7>Saccharomyces cerevisiae</TD>
<TD ALIGN="LEFT" rowspan=3>Ensembl</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/Ensembl/EF2/Saccharomyces_cerevisiae_Ensembl_EF2.tar.gz">EF2</A></TD>
<TD ALIGN="RIGHT">74 MB</TD>
<TD ALIGN="LEFT">May 15 22:35</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/Ensembl/EF3/Saccharomyces_cerevisiae_Ensembl_EF3.tar.gz">EF3</A></TD>
<TD ALIGN="RIGHT">72 MB</TD>
<TD ALIGN="LEFT">May 15 22:35</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/Ensembl/EF4/Saccharomyces_cerevisiae_Ensembl_EF4.tar.gz">EF4</A></TD>
<TD ALIGN="RIGHT">71 MB</TD>
<TD ALIGN="LEFT">May 15 22:34</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>NCBI</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/NCBI/build2.1/Saccharomyces_cerevisiae_NCBI_build2.1.tar.gz">build2.1</A></TD>
<TD ALIGN="RIGHT">70 MB</TD>
<TD ALIGN="LEFT">May 15 22:36</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/NCBI/build3.1/Saccharomyces_cerevisiae_NCBI_build3.1.tar.gz">build3.1</A></TD>
<TD ALIGN="RIGHT">70 MB</TD>
<TD ALIGN="LEFT">May 15 22:36</TD>
</TR>
<TR>
<TD ALIGN="LEFT" rowspan=2>UCSC</TD>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/UCSC/sacCer2/Saccharomyces_cerevisiae_UCSC_sacCer2.tar.gz">sacCer2</A></TD>
<TD ALIGN="RIGHT">70 MB</TD>
<TD ALIGN="LEFT">May 15 22:34</TD>
</TR>
<TR>
<TD ALIGN="LEFT"><A HREF="ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Saccharomyces_cerevisiae/UCSC/sacCer3/Saccharomyces_cerevisiae_UCSC_sacCer3.tar.gz">sacCer3</A></TD>
<TD ALIGN="RIGHT">70 MB</TD>
<TD ALIGN="LEFT">May 15 22:33</TD>
</TR>
</TABLE>
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    This research was supported in part by NIH grants R01-LM06845 and R01-GM083873 and NSF grant CCF-0347992.
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